Biomedical subjects

Marcel Swart

Publications and source records attributed to Marcel Swart.

11 recordsLinked to original sources

PubMed2006

Nucleophilic substitution at phosphorus (S(N)2@P): disappearance and reappearance of reaction barriers.

Pentacoordinate phosphorus species play a key role in organic and biological processes. Yet, their nature is still not fully understood, in particular, whether they are stable, intermediate transition complexes (TC) or labile transition states (TS). Through systematic, theoretical analyses of elementary S(N)2@C, S(N)2@Si, and S(N)2@P reactions, we show how increasing the coordination number of the central atom as well as the substituents' steric demand shifts the S(N)2@P mechanism stepwise from a single-well potential (with a stable central TC) that is common for substitution at third-period atoms, via a triple-well potential (featuring a pre- and post-TS before and after the central TC), back to the double-well potential (in which pre- and postbarrier merge into one central TS) that is well-known for substitution reactions at carbon. Our results highlight the steric nature of the S(N)2 barrier, but they also show how electronic effects modulate the barrier height.

Journal Article↗

PubMed2006

Proton affinities of maingroup-element hydrides and noble gases: trends across the periodic table, structural effects, and DFT validation.

We have carried out an extensive exploration of the gas-phase basicity of archetypal neutral bases across the periodic system using the generalized gradient approximation (GGA) of the density functional theory (DFT) at BP86/QZ4P//BP86/TZ2P. First, we validate DFT as a reliable tool for computing proton affinities and related thermochemical quantities: BP86/QZ4P//BP86/TZ2P is shown to yield a mean absolute deviation of 2.0 kcal/mol for the proton affinity at 298 K with respect to experiment, and 1.2 kcal/mol with high-level ab initio benchmark data. The main purpose of this work is to provide the proton affinities (and corresponding entropies) at 298 K of the neutral bases constituted by all maingroup-element hydrides of groups 15-17 and the noble gases, that is, group 18, and periods 1-6. We have also studied the effect of step-wise methylation of the protophilic center of the second- and third-period bases.

Journal Article↗

PubMed2005

Theoretical study of structure, pKa, lipophilicity, solubility, absorption, and polar surface area of some centrally acting antihypertensives.

The methods of theoretical chemistry have been used to elucidate the molecular properties of the substituted imidazoline and oxazoline structures, a class of potent agonists and antagonists of imidazoline receptors. The geometries of various tautomers and isomers of 2-[2,6-dichlorophenylimino]imidazolidine (clonidine), 1-(N-dicyclopropylmethyl)amino-2-oxazoline (rilmenidine), 4-chloro-N-(4,5-dihydro-1H-imidazol-2yl)-6-methoxy-2-methyl-5-pyrimidinamine (moxonidine), N-(dicyclopropylmethyl)-4,5-dihydro-1H-pyrrol-2-amine (aminopyrroline), N-dicyclopropylmethyl-4,5-dihydrothiazol-2-amine (aminothiazoline), 4,5-dihydro-2-(2-methoxyphenyl)-1H-imidazole (compound_6), 4,5-dihydro-2-(3-methylthiophen-2-yl)-1H-imidazole (compound_7), N-(2-chloro-4-iodophenyl)-4,5-dihydro-5-methyl-3H-pyrrol-2-amine (LNP_911), N-amidino-3,5-diamino-6-chloropyrazine-carboxamide (amiloride), 2-(1,4-benzodioxan-2-yl)-2-imidazoline (idazoxan), (+/-)-2-(2-ethyl-2,3-dihydro-2-benzofuranyl)-2-imidazoline (efaroxan), (4-aminobutyl)guaninine (agmatine), and 1-methyl-9H-pyrido[3,4-b]indole (harmane) have been studied using Becke3LYP/6-31+G(d,p) and BP86/TZ2P DFT methods. The optimized geometries indicate that these molecules show a distinctly nonplanar configuration of the imidazoline and oxazoline moieties. In the gas-phase, rilmenidine and aminothiazoline exist in two forms (amino and imino), the amino tautomers being more stable by about 6 kJ/mol. The calculations showed, in agreement with experiments, that clonidine, moxonidine, and LNP_911 exist in a more stable imino tautomer. The tautomer containing the amino group is by about 30 kJ/mol less stable. Computations that include the effect of solvation indicated that also in water the relative stability order of individual tautomers (amino and imino forms) is preserved. The computed pKa values varied between 6.7 and 9.0, and correlate well with the available experimental pKa's found in the literature. Among the clinically useful antihypertensives moxonidine exhibits the lowest basicity in water. At pH = 7.4 only about 50% of this drug exists in ionized form. The available experimental partition coefficients of compounds investigated are best reproduced by the CLOGP method. The computed partition coefficients varied between -1.80 (agmatine) and 5.35 (LNP_911) (CLOGP). Clonidine, moxonidine, and rilmenidine are moderately lipophilic compounds with lipophilicities between these two extreme values. The computed solubilities (about 0.1-4 g/L) show that the imidazoline and oxazoline derivatives studied have very low water solubility. The analysis of molecular descriptors defined by Lipinski has shown that most of the compounds studied obey 'rule of five'. Amiloride and agmatine 'outlets' exhibit also the lowest absorption. Therefore, in the early stages of the design of ligands acting on imidazoline binding sites, it is becoming more important to determine the pKa, lipophilicity, water solubility, polar surface area, absorption, and other physicochemical properties associated with a drug, before synthetic work is undertaken, with the aim of avoiding the synthesis of compounds that are predicted to have poor biopharmaceutical characteristics.

Adsorption↗

PubMed2005

Study of Hg22+ and complexes of NpO2+ and UO22+ in solution. examples of cation-cation interactions.

Density functional theory (BPW91/TZ2P) is used to explore the nature of cation-cation interactions (CCIs) that exist between two actinyl cations in solution. Solvation, which is modeled using COSMO, favors the complexes (ONpO-ONpO)2+ and (ONpO-OUO)3+ over separated NpO2+(aq) and UO2(2+)(aq) cations because of the quadratic dependence of solvation on charge. For (OUO-OUO)4+, solvation effects, even though very large, are unable to overcome intrinsic electrostatic repulsion between the units. The actinyl-actinyl complexes are T-shaped, with the oxygen of one unit coordinated to the actinide metal of the other unit. The association free energies of (ONpO-ONpO)2+ and (ONpO-OUO)3+ are calculated as -42.1 and -29.2 kcal/mol. Explicit consideration of the first solvation shell at the B3LYP/LANL2DZ level suggests that the free energies of binding may be overestimated. The Hg2(2+) dication, though not considered a "traditional" CCI, is very similar to the actinyl-actinyl interaction. The binding free energy of Hg2(2+) in solution is calculated as -16.0 kcal/mol.

Journal Article↗

PubMed2005

QM/MM study of the role of the solvent in the formation of the charge separated excited state in 9,9'-bianthryl.

In this paper the role of the solvent in the formation of the charge-separated excited state of 9,9'-bianthryl (BA) is examined by means of mixed molecular mechanical/quantum mechanical (QM/MM) calculations. It is shown that in weakly polar solvents a relaxed excited state is formed with an interunit angle that is significantly smaller than 90 degrees . This relaxed excited state has a considerable dipole moment even in weakly polar solvents; for benzene and dioxane dipole moments of ca. 6 D were calculated, which is close to experimental data. These dipoles are induced by the solvent in the highly polarizable relaxed excited state of BA, and the dipole relaxation time is governed by solvent reorganizations. In polar solvent the charge separation is driven to completion by the stronger dipoles in the solvent and a fully charged separated excited state is formed with an interunit angle of 90 degrees.

Journal Article↗

PubMed2005

Multicomponent synthesis of 2-imidazolines.

[reaction: see text] A multicomponent reaction (MCR) between amines, aldehydes, and isocyanides bearing an acidic alpha-proton gives easy access to a diverse range of highly substituted 2-imidazolines. The limitations of the methodology seem to be determined by the reactivity of the isocyanide and by the steric bulk on the in situ generated imine rather than by the presence of additional functional groups on the imine. Less reactive isocyanides, for example p-nitrobenzyl isocyanide 25a, react successfully with amines and aldehydes, using a catalytic amount of silver(I) acetate. Some of the resulting p-nitrophenyl-substituted 2-imidazolines undergo air oxidation to the corresponding imidazoles. Differences in reactivity of the employed isocyanides are explained with use of DFT calculations. Difficult reactions with ketones instead of aldehydes as the oxo-compound in this MCR are promoted by silver(I) acetate as well.

Journal Article↗

PubMed2005

Electronic ground states of iron porphyrin and of the first species in the catalytic reaction cycle of cytochrome P450s.

Electronic structures of iron(II) and iron(III) porphyrins are studied with density functional theory (DFT) using the GGA exchange functional OPTX in combination with the correlation functional PBE (OPBE) and with the correlation functional Perdew (OPerdew) together with a triple zeta-type basis set. These functionals, known for accurately predicting the spin ground state of iron complexes, are evaluated against other functionals for their performance in calculating relative energies for the various electronic states of both the iron porphyrins. The calculated energy orderings are triplet < quintet < singlet for the iron(II) porphyrin and quartet < sextet < doublet for the iron(III) porphyrin cation. Complexation by a thiolate ion (SH-) changes the preferred ground state for both species to high spin. This thiolate complex is used as a mimic for the cytochrome P450s active site to model the first step of the catalytic cycle of this enzyme. This first step is believed to concern the removal of an axial oxygen donating ligand from the hexacoordinated aqua-thiolate-porphyrin-iron(III) resting state. The DFT results suggest that this is not a free water molecule, because of its repulsive nature, but that it has instead hydroxy anion character. These calculations are in line with the experimentally observed change in the spin state from low to high spin upon this removal of the axial hydroxo ligand by binding of the substrate in the heme pocket of cytochrome P450.

Binding Sites↗

PubMed2005

Microscopic and macroscopic polarization within a combined quantum mechanics and molecular mechanics model.

A polarizable quantum mechanics and molecular mechanics model has been extended to account for the difference between the macroscopic electric field and the actual electric field felt by the solute molecule. This enables the calculation of effective microscopic properties which can be related to macroscopic susceptibilities directly comparable with experimental results. By separating the discrete local field into two distinct contribution we define two different microscopic properties, the so-called solute and effective properties. The solute properties account for the pure solvent effects, i.e., effects even when the macroscopic electric field is zero, and the effective properties account for both the pure solvent effects and the effect from the induced dipoles in the solvent due to the macroscopic electric field. We present results for the linear and nonlinear polarizabilities of water and acetonitrile both in the gas phase and in the liquid phase. For all the properties we find that the pure solvent effect increases the properties whereas the induced electric field decreases the properties. Furthermore, we present results for the refractive index, third-harmonic generation (THG), and electric field induced second-harmonic generation (EFISH) for liquid water and acetonitrile. We find in general good agreement between the calculated and experimental results for the refractive index and the THG susceptibility. For the EFISH susceptibility, however, the difference between experiment and theory is larger since the orientational effect arising from the static electric field is not accurately described.

Journal Article↗

PubMed2005

Calculation of the redox potential of the protein azurin and some mutants.

Azurin from Pseudomonas aeruginosa is a small 128-residue, copper-containing protein. Its redox potential can be modified by mutating the protein. Free-energy calculations based on classical molecular-dynamics simulations of the protein and from mutants in aqueous solution at different pH values were used to compute relative redox potentials. The precision of the free-energy calculations with the lambda coupling-parameter approach is evaluated as function of the number and sequence of lambda values, the sampling time and initial conditions. It is found that the precision is critically dependent on the relaxation of hydrogen-bonding networks when changing the atomic-charge distribution due to a change of redox state or pH value. The errors in the free energies range from 1 to 10 k(B)T, depending on the type of process. Only qualitative estimates of the change in redox potential by protein mutation can be obtained.

Amino Acid Substitution↗

PubMed2004

Hydrogen bonds of RNA are stronger than those of DNA, but NMR monitors only presence of methyl substituent in uracil/thymine.

Recently, Vakonakis and LiWang (J. Am. Chem. Soc. 2004, 126, 5688) reported experimental evidence for stronger hydrogen bonds in RNA A:U than in DNA A:T base pairs, which was based on differences in NMR shielding for adenine C2. We have analyzed the proposed correlation between NMR shielding and hydrogen-bond strength using density functional theory. Although we agree with the conclusion that A:U is more strongly bound, we find no correlation between the hydrogen-bond strength and the NMR shielding of C2. Our study shows that NMR merely probes the presence/absence of the methyl group in thymine/uracil, without any relation to the strength of the hydrogen bonds involved. In other words, one cannot infer the Watson-Crick hydrogen-bond strength from the NMR shielding constant of adenine C2.

Adenine↗

PubMed2003

Active site modeling in copper azurin molecular dynamics simulations.

Active site modeling in molecular dynamics simulations is investigated for the reduced state of copper azurin. Five simulation runs (5 ns each) were performed at room temperature to study the consequences of a mixed electrostatic/constrained modeling for the coordination between the metal and the polypeptide chain, using for the ligand residues a set of charges that is modified with respect to the apo form of the protein by the presence of the copper ion. The results show that the different charge values do not lead to relevant effects on the geometry of the active site of the protein, as long as bond distance constraints are used for all the five ligand atoms. The distance constraint on the O atom of Gly45 can be removed without altering the active site geometry. The coordination between Cu and the other axial ligand Met121 is outlined as being flexible. Differences are found between the bonds of the copper ion with the two apparently equivalent N(delta1) atoms of His46 and His117. The overall findings are discussed in connection with the issue of determining a model for the active site of azurin suitable to be used in molecular dynamics simulations under unfolding conditions.

Azurin↗